It's interesting. Martin layers symbolism and foreshadowing very thick. My tip has always been the direwolves, who are pretty sure indicators of what will happen to their Stark. I think of Arya and the way her wolf was "driven away." I think of Sansa and Lady being sacrificed, basically, to the Lannisters. Bran's wolf being kept isolated... etc.

Jon has the only white wolf, and it was found "after the fact." White, to me, was a big hint at the Targaryens. If you remember, Ghost also matured faster than the other direwolves. He's quiet-- doesn't make sounds-- which indicates secrets, to me. Even his name references what remains after death (Jon's parents).

It's interesting. Martin layers symbolism and foreshadowing very thick. My tip has always been the direwolves, who are pretty sure indicators of what will happen to their Stark. I think of Arya and the way her wolf was "driven away." I think of Sansa and Lady being sacrificed, basically, to the Lannisters. Bran's wolf being kept isolated... etc.

Jon has the only white wolf, and it was found "after the fact." White, to me, was a big hint at the Targaryens. If you remember, Ghost also matured faster than the other direwolves. He's quiet-- doesn't make sounds-- which indicates secrets, to me. Even his name references what remains after death (Jon's parents).

Digging this conversation.

And all the surviving direwolves are getting wilder, including Ghost. He's not always subtle about it. The vision Danys had in the House of the Undying of the man and woman who seem very likely to be Rhaegar and Lyanna is going to need some sort of explanation down the road, I think, as it was very explicit and contained a key prophecy. But as we saw with Aegon, there can be more than one surprise baby.

They all react. Arya's wolf becomes wilder and wilder out with a pack. Ghost begins to act wild as the series progresses. Shaggydog gets very wild -- and is attached to the youngest Stark. Summer also has problems and as they travel North, is drawn into violence with a wild pack. Robb's wolf devastates troops and horses. Martin is definitely drawing that line and the wolves are connected to the Starks.

...if it's him

Right, we don't know right now. But his parentage is also kind of important. Gendry's parentage is important, etc.

Having recently finished re-reading the books I have to give my two cents to this topic.

In my mind there is no doubt the Jon is the son of Lyanna Stark and Rhaegar Targaryen.
I know it cannot be completely ruled out that Ned is the father, possibly by Ashara Dayne as Barristan Selmy speculates or by an unknown "wench" as the habour master at one of The Tree Sisters believes (he has a conversation with Davos Seaworth when he is shipwrecked by Salla on his way to talk to Lord Manderly on behalf of Stannis). But most "evidence" (I guess real evidence is rare from Martin...) point to Lyanna+Rhaegar.

We know that Rhaegar wanted Lyanna and did what he could to get her. It is called an abduction and a possible rape but who says this? Lyanna apparently never did, but Robert claims it for the truth. And why not? He obviously loved her. But nothing indicates any feelings from her towards him. It was an arranged marriage and she was going to do her duty. Until Rhaegar came and proclaimed his love.
I think she ran away with Rhaegar and wanted to have his child. He even gave her 3 of the Kingsguard to protect her. We all have read about the famous fight that only Ned and Howland Reed survived. Why would Aerys (Rhaegar) send his best bodyguards and fighters to protect Lyanna in the middle of a rebellion if not to protect the royal blood? If it had just been Lyanna I am sure the Kingsguard would have stayed at Dragonstone, Kings Landing or into the field with R. It was after all The Sword of the Morning who guarded her...
She bleeds to dead. Most likely from giving birth even though Robert seems to indicate that Rhaegar killed her. She says the Ned "Promise me Ned!" and he keeps coming back to the promise(s) he made. We never hear him tell what it was but my guess is this: To take care of her child, and given that he (Jon) is a Stark it should be no problem (the family seems to have a thing for honor). To never tell Robert the truth (Robert believed to the end that she loved him and why ruin his friend's joy?). Robert would obviously have gone crazy and tried to kill the child. For personal reasons and to destroy the last available Targaryen. And I am not sure the relationship between Stark and Baratheon would not have been tainted just a little bit by the betrayal Robert would have seen.

So all in all Ned did his duty. To his House (by keeping Lyanna's secret), to his blood (by protecting the child) and to his king (by hiding the true origin of Jon from everybody). Jon lived and Robert reigned. And know Ned is dead and no one can tell the truth. Oh wait, one person can. And he has been absent for 5 books despite a very interesting backstory. Well maybe his children know something and can tell Bran while they wait for winter to come...

I only just read this theory yesterday. It'd never even crossed my mind because I hadn't bothered to study the story in minute detail. In other things that I read I do go into great depth, becoming an expert on the text, but with Martin I just enjoyed the ride.

I like the theory, and it probably all makes sense based on the subtextual clues. But I'm also of the opinion that the writer of the story should not necessarily dot every i and cross every t: this means that every single thing written shouldn't be absolutely part of the larger story. Life doesn't work like that and, therefore, a story should have elements which are tangents that don't really matter and where sub-plots don't resolve. Since Martin seems to also be one of the pioneers of this gritty real-life style of fantasy story-telling, I would think that he might be mindful of this.

Based on what I know of history, when events like those depicted in Ice and Fire happen, the person who ends up on top is some random who wasn't involved in the initial plot and therefore expended few resources while the other powerful people exhausted themselves. After one of the initial people came out on top, they generally make too many changes for those remaining to accept and are too weak to resist when the random steps in and unseats them.

Of course, I don't expect this outcome from Martin. He doesn't really go that far with the realism.

Not necessarily. There must always be three. But then he suddenly pulled one of Elya's children in book 5, so it's hard to know really where he might hide another. So you can't count them and say, oh, one is missing, it must be Jon.
Igor